Evidence claim

mRNABench against non-coding RNA benchmarks on DNABERT-2 and RNA-FM: different sequence domain

Discrepancy review of DNABERT2 · mRNABench ECLIP · AUPRC (%)

explained

Review of discrepancy-14ca3a59b4201d63: explained.

Evidence

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Evidence table

Inspect claims, sources and review details

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25 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Action investigated Context-only references	mRNABench: A curated benchmark for mature mRNA property and function prediction Original source ↗ The outlier and consensus results of discrepancy-14ca3a59b4201d63 as published at https://benchmarks.rewirebio.io/contested/discrepancy-14ca3a59b4201d63/ (release 2026-10-23-968c8720eea6) Version: preprint archived 2025-07-08 Retrieved: 2026-09-16T10:41:16.497221+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.action` Source artifact SHA-256: `79f6264ee883535203c63a313547e7c57baa85585f76b42f8d899eb17fb7e600` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Date 2026-10-23 Context-only references	mRNABench: A curated benchmark for mature mRNA property and function prediction Original source ↗ The outlier and consensus results of discrepancy-14ca3a59b4201d63 as published at https://benchmarks.rewirebio.io/contested/discrepancy-14ca3a59b4201d63/ (release 2026-10-23-968c8720eea6) Version: preprint archived 2025-07-08 Retrieved: 2026-09-16T10:41:16.497221+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.date` Source artifact SHA-256: `79f6264ee883535203c63a313547e7c57baa85585f76b42f8d899eb17fb7e600` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Discrepancy id discrepancy-14ca3a59b4201d63 Context-only references	mRNABench: A curated benchmark for mature mRNA property and function prediction Original source ↗ The outlier and consensus results of discrepancy-14ca3a59b4201d63 as published at https://benchmarks.rewirebio.io/contested/discrepancy-14ca3a59b4201d63/ (release 2026-10-23-968c8720eea6) Version: preprint archived 2025-07-08 Retrieved: 2026-09-16T10:41:16.497221+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.discrepancy_id` Source artifact SHA-256: `79f6264ee883535203c63a313547e7c57baa85585f76b42f8d899eb17fb7e600` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Claimed field discrepancy_review Context-only references	mRNABench: A curated benchmark for mature mRNA property and function prediction Original source ↗ The outlier and consensus results of discrepancy-14ca3a59b4201d63 as published at https://benchmarks.rewirebio.io/contested/discrepancy-14ca3a59b4201d63/ (release 2026-10-23-968c8720eea6) Version: preprint archived 2025-07-08 Retrieved: 2026-09-16T10:41:16.497221+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `79f6264ee883535203c63a313547e7c57baa85585f76b42f8d899eb17fb7e600` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Investigation url https://github.com/rewire-bio/rewire-benchmark-data/issues/202 Context-only references	mRNABench: A curated benchmark for mature mRNA property and function prediction Original source ↗ The outlier and consensus results of discrepancy-14ca3a59b4201d63 as published at https://benchmarks.rewirebio.io/contested/discrepancy-14ca3a59b4201d63/ (release 2026-10-23-968c8720eea6) Version: preprint archived 2025-07-08 Retrieved: 2026-09-16T10:41:16.497221+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.investigation_url` Source artifact SHA-256: `79f6264ee883535203c63a313547e7c57baa85585f76b42f8d899eb17fb7e600` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Rationale mRNABench probes frozen embeddings on mature mRNA properties (half-life, ribosome load, localisation, eCLIP, GO terms, variant effects). The consensus is Wang et al. 2026 zero-shot non-coding RNA tasks (RNAGym ncRNA DMS, Rfam families, ArchiveII RNA types) and You et al. 2026 fine-tuned splice-site classification. RNA-FM was trained on non-coding RNA; DNABERT-2 on whole genomes. Three of the seven mRNABench wins are 1.2 to 2.7 percent apart and no error bars are reported. RNA-FM's input length limit, which would truncate most full-length mRNAs, has not yet been checked (issue 202). Context-only references	mRNABench: A curated benchmark for mature mRNA property and function prediction Original source ↗ The outlier and consensus results of discrepancy-14ca3a59b4201d63 as published at https://benchmarks.rewirebio.io/contested/discrepancy-14ca3a59b4201d63/ (release 2026-10-23-968c8720eea6) Version: preprint archived 2025-07-08 Retrieved: 2026-09-16T10:41:16.497221+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.rationale` Source artifact SHA-256: `79f6264ee883535203c63a313547e7c57baa85585f76b42f8d899eb17fb7e600` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Revision 1 Context-only references	mRNABench: A curated benchmark for mature mRNA property and function prediction Original source ↗ The outlier and consensus results of discrepancy-14ca3a59b4201d63 as published at https://benchmarks.rewirebio.io/contested/discrepancy-14ca3a59b4201d63/ (release 2026-10-23-968c8720eea6) Version: preprint archived 2025-07-08 Retrieved: 2026-09-16T10:41:16.497221+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.revision` Source artifact SHA-256: `79f6264ee883535203c63a313547e7c57baa85585f76b42f8d899eb17fb7e600` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Source location The outlier and consensus results of discrepancy-14ca3a59b4201d63 as published at https://benchmarks.rewirebio.io/contested/discrepancy-14ca3a59b4201d63/ (release 2026-10-23-968c8720eea6) Context-only references	mRNABench: A curated benchmark for mature mRNA property and function prediction Original source ↗ The outlier and consensus results of discrepancy-14ca3a59b4201d63 as published at https://benchmarks.rewirebio.io/contested/discrepancy-14ca3a59b4201d63/ (release 2026-10-23-968c8720eea6) Version: preprint archived 2025-07-08 Retrieved: 2026-09-16T10:41:16.497221+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `79f6264ee883535203c63a313547e7c57baa85585f76b42f8d899eb17fb7e600` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Claimed value explained Context-only references	mRNABench: A curated benchmark for mature mRNA property and function prediction Original source ↗ The outlier and consensus results of discrepancy-14ca3a59b4201d63 as published at https://benchmarks.rewirebio.io/contested/discrepancy-14ca3a59b4201d63/ (release 2026-10-23-968c8720eea6) Version: preprint archived 2025-07-08 Retrieved: 2026-09-16T10:41:16.497221+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.value` Source artifact SHA-256: `79f6264ee883535203c63a313547e7c57baa85585f76b42f8d899eb17fb7e600` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Description Review of discrepancy-14ca3a59b4201d63: explained. Context-only references	mRNABench: A curated benchmark for mature mRNA property and function prediction Original source ↗ The outlier and consensus results of discrepancy-14ca3a59b4201d63 as published at https://benchmarks.rewirebio.io/contested/discrepancy-14ca3a59b4201d63/ (release 2026-10-23-968c8720eea6) Version: preprint archived 2025-07-08 Retrieved: 2026-09-16T10:41:16.497221+00:00	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `79f6264ee883535203c63a313547e7c57baa85585f76b42f8d899eb17fb7e600` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact

How to read the evidence

Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

1 source record and release history

mRNABench: A curated benchmark for mature mRNA property and function prediction · Original source · preprint archived 2025-07-08

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Technical metadata and extraction receipts

Stable ID: discrepancy-review-20261023-mrnabench-dnabert2-rnafm

areas: rna-transcriptomes
contexts: research
field: discrepancy_review
discrepancy id: discrepancy-14ca3a59b4201d63
revision: 1
value: explained
action: investigated
date: 2026-10-23
rationale: mRNABench probes frozen embeddings on mature mRNA properties (half-life, ribosome load, localisation, eCLIP, GO terms, variant effects). The consensus is Wang et al. 2026 zero-shot non-coding RNA tasks (RNAGym ncRNA DMS, Rfam families, ArchiveII RNA types) and You et al. 2026 fine-tuned splice-site classification. RNA-FM was trained on non-coding RNA; DNABERT-2 on whole genomes. Three of the seven mRNABench wins are 1.2 to 2.7 percent apart and no error bars are reported. RNA-FM's input length limit, which would truncate most full-length mRNAs, has not yet been checked (issue 202).
investigation url: https://github.com/rewire-bio/rewire-benchmark-data/issues/202
source locator: The outlier and consensus results of discrepancy-14ca3a59b4201d63 as published at https://benchmarks.rewirebio.io/contested/discrepancy-14ca3a59b4201d63/ (release 2026-10-23-968c8720eea6)
review: method: automated-source-review; ai-assisted-source-review; reviewer: claude; reviewer note: Recorded by a Claude agent; no human review claimed.; date: 2026-10-23; method note: Read every outlier and consensus result of the finding, with its protocol, metric, configuration and source, from the published contested-result page, and compared the tasks, settings and configurations on each side. The original papers were not re-opened.; note: Records where the discrepancy stands, not a correction to any result. No result value or status was changed.

Related records

subject: DNABERT2 · mRNABench ECLIP · AUPRC (%)
subject: DNABERT2 · mRNABench GO · AUPRC (%)
subject: DNABERT2 · mRNABench HL · R
subject: DNABERT2 · mRNABench MRL-HL-PAIR · R
subject: DNABERT2 · mRNABench MRL-MPRA · R
subject: DNABERT2 · mRNABench MRNA-LOC-LR · AUPRC (%)
subject: DNABERT2 · mRNABench VEP · AUPRC (%)
subject: RNA-FM · mRNABench ECLIP · AUPRC (%)
subject: RNA-FM · mRNABench GO · AUPRC (%)
subject: RNA-FM · mRNABench HL · R
subject: RNA-FM · mRNABench MRL-HL-PAIR · R
subject: RNA-FM · mRNABench MRL-MPRA · R
subject: RNA-FM · mRNABench MRNA-LOC-LR · AUPRC (%)
subject: RNA-FM · mRNABench VEP · AUPRC (%)

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